Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 8 of 290
Found at i:2312233 original size:46 final size:46
Alignment explanation
Indices: 2312163--2312257 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 46
2312153 ATGCCGTAAA
* * * *
2312163 TATCGCAGCAACGCTGCTAGTTAACAGAATGACTATAACCCATAAG
1 TATCGCAACAACGCTGCCAATTAACAGAACGACTATAACCCATAAG
* *
2312209 TATCGCAACAATGCTGCCAATTAACAGAACGACTATAAGCCATAAG
1 TATCGCAACAACGCTGCCAATTAACAGAACGACTATAACCCATAAG
2312255 TAT
1 TAT
2312258 TGTAGAAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (46 bp):
TATCGCAACAACGCTGCCAATTAACAGAACGACTATAACCCATAAG
Found at i:2314543 original size:56 final size:56
Alignment explanation
Indices: 2314476--2314707 Score: 455
Period size: 56 Copynumber: 4.1 Consensus size: 56
2314466 TATTAGTTTA
*
2314476 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2314532 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2314588 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2314644 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2314700 TTGCCCAT
1 TTGCCCAT
2314708 CATCCCTTGT
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 175 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:2315121 original size:43 final size:43
Alignment explanation
Indices: 2315054--2315212 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
2315044 AGCTGGTACA
* ** * *
2315054 ATGCCAATGTCCCAGGCGTGGTCTTACATGTAATCAAATATCG
1 ATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAATATCG
* *
2315097 ATGCCACTGTCCCAAACA-GAGTCTTACACGAAATCATATA-CG
1 ATGCCACTGTCCCAAACATG-GTCTTACACGTAATCAAATATCG
* * *
2315139 ATGCCAATGTCCCAGACATGGTCTTACGCGTAAATCACAA-ATCG
1 ATGCCACTGTCCCAAACATGGTCTTACACGT-AATCA-AATATCG
* *
2315183 ATGCCAAC-GTCCCAGACGTGGTCTTACACG
1 ATGCC-ACTGTCCCAAACATGGTCTTACACG
2315213 ATAACACATA
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
42 28 0.29
43 38 0.40
44 28 0.29
45 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAATATCG
Found at i:2315207 original size:86 final size:85
Alignment explanation
Indices: 2315054--2315213 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 85
2315044 AGCTGGTACA
* * *
2315054 ATGCCAATGTCCCAGGCGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAAACAGAGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAACAGAGT
2315119 CTTACACGAAATCATATACG
66 CTTACACGAAATCATATACG
* *
2315139 ATGCCAATGTCCCAGACATGGTCTTACGCGTAAATCACAA-ATCGATGCCAAC-GTCCCAGAC-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AATCA-AATATCGATGCC-ACTGTCCCAAACAG
*
2315201 TGGTCTTACACGA
63 -AGTCTTACACGA
2315214 TAACACATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
85 28 0.43
86 33 0.51
87 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (85 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAACAGAGT
CTTACACGAAATCATATACG
Found at i:2319891 original size:41 final size:41
Alignment explanation
Indices: 2319844--2319926 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
2319834 CTGAATAGAT
*
2319844 AATTTAGTTAGGGCTAACTTCTTCTATAACAATGTCTTTGC
1 AATTTAGTCAGGGCTAACTTCTTCTATAACAATGTCTTTGC
*
2319885 AATTTAGTCAGGGTTAACTTCTTCTATAACAATGTCTTTGC
1 AATTTAGTCAGGGCTAACTTCTTCTATAACAATGTCTTTGC
2319926 A
1 A
2319927 TAATCTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (41 bp):
AATTTAGTCAGGGCTAACTTCTTCTATAACAATGTCTTTGC
Found at i:2322577 original size:21 final size:22
Alignment explanation
Indices: 2322551--2322594 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2322541 TTTATTCATG
2322551 TTTCATTTACACATAC-TCACA
1 TTTCATTTACACATACATCACA
* *
2322572 TTTCATTTCCATATACATCACA
1 TTTCATTTACACATACATCACA
2322594 T
1 T
2322595 AACATTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTCATTTACACATACATCACA
Found at i:2322857 original size:42 final size:44
Alignment explanation
Indices: 2322756--2322915 Score: 179
Period size: 43 Copynumber: 3.7 Consensus size: 44
2322746 AGCTCGTATA
* * * * *
2322756 ATGCCAACGTCCCAGA-TGTGGTCTTACATGTAATCAAATATTG
1 ATGCCAATGTCCCAGACAGTGGTCTTACACGAAATCAAATATCG
* *
2322799 ATGCCATTGTCCCAGACAG-GGTCTTACACGAAATCATATA-CG
1 ATGCCAATGTCCCAGACAGTGGTCTTACACGAAATCAAATATCG
*
2322841 ATGCCAATGTCCCAGACA-TGGTCTTACACGTAAATCACAA-ATCA
1 ATGCCAATGTCCCAGACAGTGGTCTTACACG-AAATCA-AATATCG
*
2322885 ATGCCAATGTCCCAAAC-GTGGTCTTACACGA
1 ATGCCAATGTCCCAGACAGTGGTCTTACACGA
2322916 TAACACATAT
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
42 29 0.29
43 40 0.40
44 31 0.31
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACAGTGGTCTTACACGAAATCAAATATCG
Found at i:2322910 original size:86 final size:85
Alignment explanation
Indices: 2322756--2322915 Score: 207
Period size: 86 Copynumber: 1.9 Consensus size: 85
2322746 AGCTCGTATA
** * ** * *
2322756 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAAATATTGATGCCATTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCAATGCCAATGTCCCAAACAGGGT
2322821 CTTACACGAAATCATATACG
66 CTTACACGAAATCATATACG
*
2322841 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAA-ATCAATGCCAATGTCCCAAAC-GT
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATCA-AATATCAATGCCAATGTCCCAAACAG-
2322904 GGTCTTACACGA
63 GGTCTTACACGA
2322916 TAACACATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
85 28 0.44
86 34 0.53
87 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCAATGCCAATGTCCCAAACAGGGT
CTTACACGAAATCATATACG
Found at i:2327404 original size:37 final size:37
Alignment explanation
Indices: 2327354--2327427 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2327344 TAGTTACTCA
2327354 AAAATTCAAGAAATATGAGATTAAACTATACAAGTGT
1 AAAATTCAAGAAATATGAGATTAAACTATACAAGTGT
2327391 AAAATTCAAGAAATATGAGATTAAACTATACAAGTGT
1 AAAATTCAAGAAATATGAGATTAAACTATACAAGTGT
2327428 GACTATTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (37 bp):
AAAATTCAAGAAATATGAGATTAAACTATACAAGTGT
Found at i:2331661 original size:18 final size:18
Alignment explanation
Indices: 2331638--2331675 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2331628 AAGGTAAGAG
2331638 TTGAAGAGAATTGCCTTT
1 TTGAAGAGAATTGCCTTT
2331656 TTGAAGAGAATTGCCTTT
1 TTGAAGAGAATTGCCTTT
2331674 TT
1 TT
2331676 CTTTTCACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (18 bp):
TTGAAGAGAATTGCCTTT
Found at i:2334653 original size:46 final size:46
Alignment explanation
Indices: 2334597--2334954 Score: 299
Period size: 46 Copynumber: 7.7 Consensus size: 46
2334587 TTGGGCATCT
*
2334597 GAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * *
2334643 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TCC
2334690 GAACTCGTTGAG-TGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * * *
2334735 GAACTCATTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TCC
* *
2334782 GAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * * * * * * *
2334828 GAACTAGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-ACGTCC
* *
2334875 GAGA-TCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCC
1 GA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * *
2334921 GAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2334955 GCGGGTTACA
Statistics
Matches: 246, Mismatches: 40, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
42 6 0.02
43 8 0.03
45 21 0.09
46 116 0.47
47 76 0.31
48 5 0.02
49 4 0.02
50 7 0.03
51 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
Found at i:2334700 original size:93 final size:93
Alignment explanation
Indices: 2334590--2334947 Score: 596
Period size: 93 Copynumber: 3.9 Consensus size: 93
2334580 CGGATATTTG
* * *
2334590 GGCATCTGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
2334655 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
2334683 GGCATCCGAACTCGTTGAG-TGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
2334747 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
2334775 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACT-AGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCA-TTGA
*
2334839 GTTGAGTCCGAGTTCGTGAAATGTAACTA
65 GTTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
2334868 GGCATCCGAGA-TCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGA
1 GGCATCCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGA
2334932 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
2334948 CTTATGGGCG
Statistics
Matches: 250, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
92 90 0.36
93 159 0.64
94 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:2334796 original size:47 final size:47
Alignment explanation
Indices: 2334640--2334900 Score: 249
Period size: 47 Copynumber: 5.6 Consensus size: 47
2334630 GATGCGAACG
2334640 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * *
2334687 TCCGAACTCGTTGAG-TGAGTCCGAGTTCACTTATGGATGCGAAC---G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
*
2334732 TCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * * * *
2334779 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
* *
2334825 TCCGAACTAGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
*
2334872 TCCGAGA-TCGTTGAGTTGAGTCTGAGTTC
1 TCCGA-ACTCGTTGAGTTGAGTCCGAGTTC
2334901 ACTTATGGAT
Statistics
Matches: 173, Mismatches: 21, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
42 6 0.03
43 7 0.04
45 20 0.12
46 53 0.31
47 69 0.40
48 4 0.02
49 4 0.02
50 7 0.04
51 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:2340090 original size:33 final size:34
Alignment explanation
Indices: 2340048--2340117 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
2340038 AGTAATAGTC
*
2340048 CAGTATCAGT-TAGGGCCTTAGCCC-ATTCAGTAA
1 CAGTATCAGTGT-GAGCCTTAGCCCAATTCAGTAA
2340081 CAGTATCAGTGTGAGCCTTAGCCCAATTCAGTAA
1 CAGTATCAGTGTGAGCCTTAGCCCAATTCAGTAA
2340115 CAG
1 CAG
2340118 CACAGTACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
CAGTATCAGTGTGAGCCTTAGCCCAATTCAGTAA
Found at i:2342416 original size:132 final size:132
Alignment explanation
Indices: 2342180--2342576 Score: 742
Period size: 132 Copynumber: 3.0 Consensus size: 132
2342170 ACTGAAGCAA
2342180 GCATGCATTTATGCAACACAACACAC-AAAAAAATTATTAAAGATTTGGGGCATTACAACTCTAC
1 GCATGCATTTATGCAACACAACACACAAAAAAAATTATTAAAGATTTGGGGCATTACAACTCTAC
2342244 CCCCTAAAATAAAATTTCGGCCTCGAAATTTACCTGTCAAAACAGATGAGGGTATTGTTGTCGTA
66 CCCCTAAAATAAAATTTCGGCCTCGAAATTTACCTGTCAAAACAGATGAGGGTATTGTTGTCGTA
2342309 TC
131 TC
2342311 GCATGCATTTATGCAACACAACACACAAAAAAAATTATTAAAGATTTGGGGCATTACAACTCTAC
1 GCATGCATTTATGCAACACAACACACAAAAAAAATTATTAAAGATTTGGGGCATTACAACTCTAC
* *
2342376 CCCCTAAAATAAAATTTCAGCCTTGAAATTTACCTGTCAAAACAGATGAGGGTATTGTTGTCGTA
66 CCCCTAAAATAAAATTTCGGCCTCGAAATTTACCTGTCAAAACAGATGAGGGTATTGTTGTCGTA
2342441 TC
131 TC
* *
2342443 GCATGCATTTATGCAACACAACACACAAAAAAATTTATTAAAGATTTGGGGCATTACAACTTTAC
1 GCATGCATTTATGCAACACAACACACAAAAAAAATTATTAAAGATTTGGGGCATTACAACTCTAC
*
2342508 CCCCTAAAATAAAATTTCGGCCTCGAAATTTACCTATCAAAACAGATGAGGGTATTGTTGTCGTA
66 CCCCTAAAATAAAATTTCGGCCTCGAAATTTACCTGTCAAAACAGATGAGGGTATTGTTGTCGTA
2342573 TC
131 TC
2342575 GC
1 GC
2342577 CTCCTTGGGT
Statistics
Matches: 258, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
131 26 0.10
132 232 0.90
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (132 bp):
GCATGCATTTATGCAACACAACACACAAAAAAAATTATTAAAGATTTGGGGCATTACAACTCTAC
CCCCTAAAATAAAATTTCGGCCTCGAAATTTACCTGTCAAAACAGATGAGGGTATTGTTGTCGTA
TC
Found at i:2348463 original size:27 final size:27
Alignment explanation
Indices: 2348419--2348470 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2348409 ATCATACAAA
* *
2348419 TCATAGGGACATATCAGTTATTTTACC
1 TCATAGGGACATAACAGTCATTTTACC
* *
2348446 TCATAGGGGCGTAACAGTCATTTTA
1 TCATAGGGACATAACAGTCATTTTA
2348471 TTAAATGGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (27 bp):
TCATAGGGACATAACAGTCATTTTACC
Found at i:2373378 original size:3 final size:3
Alignment explanation
Indices: 2373370--2373403 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2373360 TTTTATTTGT
*
2373370 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2373404 ATAACAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2374094 original size:21 final size:21
Alignment explanation
Indices: 2374070--2374137 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
2374060 CTTCAACAGA
2374070 CCCAATCACCAAC-CCGACAAC
1 CCCAATCA-CAACTCCGACAAC
* *
2374091 CCCAGTCACAACTCCGACAGC
1 CCCAATCACAACTCCGACAAC
* * *
2374112 ACCAGTTACAACTCCGACAAC
1 CCCAATCACAACTCCGACAAC
2374133 CCCAA
1 CCCAA
2374138 CCCCGACTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.35, C:0.47, G:0.09, T:0.09
Consensus pattern (21 bp):
CCCAATCACAACTCCGACAAC
Found at i:2374721 original size:18 final size:18
Alignment explanation
Indices: 2374695--2374729 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2374685 TACCATGACC
2374695 ATGACCCCACCCTTTCCG
1 ATGACCCCACCCTTTCCG
* *
2374713 ATGAGCCCACCTTTTCC
1 ATGACCCCACCCTTTCC
2374730 CGGAGCAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.46, G:0.11, T:0.26
Consensus pattern (18 bp):
ATGACCCCACCCTTTCCG
Found at i:2377731 original size:4 final size:4
Alignment explanation
Indices: 2377722--2377752 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2377712 TACATAATAT
*
2377722 TATG TATG TATG TATG TATA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
2377753 CCAACTCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2377739 original size:12 final size:12
Alignment explanation
Indices: 2377718--2377752 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2377708 TTTTTACATA
2377718 ATAT-TATGTAT
1 ATATGTATGTAT
*
2377729 GTATGTATGTAT
1 ATATGTATGTAT
2377741 ATATGTATGTAT
1 ATATGTATGTAT
2377753 CCAACTCCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 3 0.14
12 18 0.86
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (12 bp):
ATATGTATGTAT
Found at i:2380844 original size:38 final size:37
Alignment explanation
Indices: 2380793--2380869 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 37
2380783 TGAAATTAGA
* *
2380793 AATCTATTCTCCCTCTCAATTTCCCTACCCCTCCTGT
1 AATCTATTCTCCCTCCCAATTTCCCTACACCTCCTGT
2380830 NAATCTATTCTCCCTCCCAATTTCCCTACACCTCCTGT
1 -AATCTATTCTCCCTCCCAATTTCCCTACACCTCCTGT
2380868 AA
1 AA
2380870 ATTGTTGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.19, C:0.42, G:0.03, T:0.35
Consensus pattern (37 bp):
AATCTATTCTCCCTCCCAATTTCCCTACACCTCCTGT
Found at i:2384645 original size:70 final size:70
Alignment explanation
Indices: 2384558--2384769 Score: 406
Period size: 70 Copynumber: 3.0 Consensus size: 70
2384548 TTAATAATGA
2384558 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
2384623 CCTGG
66 CCTGG
2384628 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
2384693 CCTGG
66 CCTGG
* *
2384698 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAGGAAACTGTCAATTGAAGAGCT
1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
2384763 CCTGG
66 CCTGG
2384768 AA
1 AA
2384770 CATACTGCAT
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 140 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (70 bp):
AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
CCTGG
Found at i:2389308 original size:19 final size:21
Alignment explanation
Indices: 2389270--2389319 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2389260 AATACATTAA
* *
2389270 ATTAAAAAATAACTCTTAATT
1 ATTAAAAAATAACACATAATT
2389291 -TTAAAAAATAA-ACATAATT
1 ATTAAAAAATAACACATAATT
2389310 ATCTAAAAAA
1 AT-TAAAAAA
2389320 ATTAAATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAAAAAATAACACATAATT
Found at i:2391235 original size:29 final size:29
Alignment explanation
Indices: 2391192--2391251 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
2391182 AATACATTAA
2391192 ATCCAAACAGACCTAAGCAAACCTATCAT
1 ATCCAAACAGACCTAAGCAAACCTATCAT
* * *
2391221 ATCCAAACAGTCCTAGGCACACCTATCAT
1 ATCCAAACAGACCTAAGCAAACCTATCAT
2391250 AT
1 AT
2391252 AAGCTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.20
Consensus pattern (29 bp):
ATCCAAACAGACCTAAGCAAACCTATCAT
Found at i:2394355 original size:15 final size:15
Alignment explanation
Indices: 2394335--2394376 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
2394325 TGTCCTTGAA
2394335 GGATGTTCCCCATAT
1 GGATGTTCCCCATAT
2394350 GGATGTTCCCCATAT
1 GGATGTTCCCCATAT
2394365 GGATGTTCCCCA
1 GGATGTTCCCCA
2394377 GCAATGGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (15 bp):
GGATGTTCCCCATAT
Found at i:2403490 original size:15 final size:15
Alignment explanation
Indices: 2403456--2403489 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2403446 AATTCTAAAA
*
2403456 ATTTAAAAAAAATAT
1 ATTTTAAAAAAATAT
2403471 ATTTTAAAAAAATA-
1 ATTTTAAAAAAATAT
2403485 ATTTT
1 ATTTT
2403490 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAAAAAATAT
Found at i:2404063 original size:6 final size:7
Alignment explanation
Indices: 2404046--2404071 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2404036 CATTTAATAT
2404046 TTTTTTC
1 TTTTTTC
2404053 TTTTTTC
1 TTTTTTC
2404060 TTTTTTC
1 TTTTTTC
2404067 TTTTT
1 TTTTT
2404072 AAGTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:2409521 original size:2 final size:2
Alignment explanation
Indices: 2409514--2409555 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2409504 CGAATATCCC
2409514 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2409556 GTGCCTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2410884 original size:8 final size:8
Alignment explanation
Indices: 2410871--2410896 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2410861 ATTAATAATA
2410871 TATAAAAT
1 TATAAAAT
2410879 TATAAAAT
1 TATAAAAT
2410887 TATAAAAT
1 TATAAAAT
2410895 TA
1 TA
2410897 AATAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATAAAAT
Found at i:2430752 original size:25 final size:25
Alignment explanation
Indices: 2430724--2430771 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2430714 GAGATTTTAG
2430724 AAAAGAGAAAAAAGAAGAGAGAGAA
1 AAAAGAGAAAAAAGAAGAGAGAGAA
* * *
2430749 AAAAGCGAGAAGAGAAGAGAGAG
1 AAAAGAGAAAAAAGAAGAGAGAG
2430772 TGAGAGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (25 bp):
AAAAGAGAAAAAAGAAGAGAGAGAA
Found at i:2430762 original size:16 final size:15
Alignment explanation
Indices: 2430722--2430764 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2430712 GAGAGATTTT
2430722 AGAA-AAGAGAAAAA
1 AGAAGAAGAGAAAAA
2430736 AGAAGAGAGAGAAAAA
1 AGAAGA-AGAGAAAAA
*
2430752 AGCGAGAAGAGAA
1 AG-AAGAAGAGAA
2430765 GAGAGAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 1 0.04
16 17 0.68
17 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAGAAAAA
Found at i:2431738 original size:14 final size:14
Alignment explanation
Indices: 2431719--2431746 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2431709 TTTTTGGCCC
2431719 CCATAAATGATATA
1 CCATAAATGATATA
2431733 CCATAAATGATATA
1 CCATAAATGATATA
2431747 TTTTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
CCATAAATGATATA
Found at i:2432667 original size:22 final size:22
Alignment explanation
Indices: 2432642--2432684 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2432632 AGCATATGAG
2432642 AAAACTTGGTAAAAAATGTACT
1 AAAACTTGGTAAAAAATGTACT
2432664 AAAACTTGGTAAAAAATGTAC
1 AAAACTTGGTAAAAAATGTAC
2432685 AAGCTATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAACTTGGTAAAAAATGTACT
Found at i:2433442 original size:32 final size:31
Alignment explanation
Indices: 2433406--2433467 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2433396 AAGTTAAGAG
* * *
2433406 AAAAATATTTTTAGATCCCTTAAAAATTAATA
1 AAAAAAATTTTT-GAACCCTTAAAAACTAATA
*
2433438 AAAAAAATTTTTGAACTCTTAAAAACTAAT
1 AAAAAAATTTTTGAACCCTTAAAAACTAAT
2433468 TTTTTTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAAAAATTTTTGAACCCTTAAAAACTAATA
Found at i:2447513 original size:15 final size:16
Alignment explanation
Indices: 2447493--2447537 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
2447483 TTCTTTATTA
*
2447493 AATATTATTATTTCT-
1 AATATTATTATTTATC
2447508 AATATTATTAATATTATC
1 AATATTATT-AT-TTATC
2447526 AATATTATTATT
1 AATATTATTATT
2447538 ATTTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 5 0.19
18 9 0.35
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATTATTATTTATC
Found at i:2447519 original size:9 final size:9
Alignment explanation
Indices: 2447487--2447554 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
2447477 TTTTGTTTCT
2447487 TTATTAAATA
1 TTATT-AATA
2447497 TTATT-AT-
1 TTATTAATA
*
2447504 TT-CTAATA
1 TTATTAATA
2447512 TTATTAATA
1 TTATTAATA
*
2447521 TTATCAATA
1 TTATTAATA
*
2447530 TTATTATTA
1 TTATTAATA
* *
2447539 TTTTTTATA
1 TTATTAATA
2447548 -TATTAAT
1 TTATTAAT
2447555 GTATATTTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
8 9 0.20
9 26 0.58
10 5 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATTAATA
Found at i:2447522 original size:18 final size:18
Alignment explanation
Indices: 2447495--2447554 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2447485 CTTTATTAAA
*
2447495 TATTATTATTTCTAATAT
1 TATTAATATTTCTAATAT
2447513 TATTAATATTATC-AATAT
1 TATTAATATT-TCTAATAT
* * *
2447531 TATTATTATTTTTTATA-
1 TATTAATATTTCTAATAT
2447548 TATTAAT
1 TATTAAT
2447555 GTATATTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.20
18 26 0.74
19 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTAATATTTCTAATAT
Found at i:2447628 original size:12 final size:11
Alignment explanation
Indices: 2447608--2447729 Score: 54
Period size: 12 Copynumber: 10.6 Consensus size: 11
2447598 TTTAATTTCA
2447608 TATTATTATTAT
1 TATTATTA-TAT
* *
2447620 TAGTATTATAA
1 TATTATTATAT
2447631 TATTA-TAT-T
1 TATTATTATAT
2447640 TATTATTAATAT
1 TATTATT-ATAT
*
2447652 TAGTATATATAT
1 TATTAT-TATAT
*
2447664 T-TTATTAT-G
1 TATTATTATAT
2447673 TATGTATATATAT
1 TAT-TAT-TATAT
* *
2447686 AATTTTTATAT
1 TATTATTATAT
** *
2447697 AGTATTATCGTTT
1 --TATTATTATAT
2447710 CTATTATTATATT
1 -TATTATTATA-T
2447723 TATTATT
1 TATTATT
2447730 TTCACTATTA
Statistics
Matches: 80, Mismatches: 19, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
9 6 0.08
10 8 0.10
11 19 0.24
12 37 0.46
13 10 0.12
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (11 bp):
TATTATTATAT
Found at i:2447633 original size:23 final size:24
Alignment explanation
Indices: 2447607--2447704 Score: 87
Period size: 26 Copynumber: 4.0 Consensus size: 24
2447597 CTTTAATTTC
2447607 ATAT-TATTATTATTAGTATTATA
1 ATATATATTATTATTAGTATTATA
*
2447630 ATATTATATTTATTATTAATATTAGT-
1 ATA-TATA-TTATTATTAGTATTA-TA
2447656 ATATATATT-TTATTATGTATGTAT-
1 ATATATATTATTATTA-GTAT-TATA
*
2447680 ATATATAATTTTTATATAGTATTAT
1 ATATAT-ATTATTAT-TAGTATTAT
2447705 CGTTTCTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
23 9 0.14
24 13 0.20
25 14 0.22
26 25 0.39
27 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
ATATATATTATTATTAGTATTATA
Found at i:2447931 original size:38 final size:41
Alignment explanation
Indices: 2447880--2447962 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 41
2447870 TTAATACTCT
* * *
2447880 TATATTATGTATAT-TATTTTTT-TAATATTATATT-TTTA
1 TATATTACGTATATATATTTTTTAAAATATCATATTATTTA
2447918 TATATTACGTATATATATTTTTTAAAATATCATATTATTTA
1 TATATTACGTATATATATTTTTTAAAATATCATATTATTTA
2447959 TATA
1 TATA
2447963 CTTTATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 13 0.33
39 8 0.21
40 10 0.26
41 8 0.21
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (41 bp):
TATATTACGTATATATATTTTTTAAAATATCATATTATTTA
Found at i:2447973 original size:38 final size:35
Alignment explanation
Indices: 2447879--2447973 Score: 86
Period size: 38 Copynumber: 2.5 Consensus size: 35
2447869 TTTAATACTC
*
2447879 TTATATTATGTATATTAT-TTTTTTAATATTATATTT
1 TTATA-TAT-TATATTATATTTTTTAATATCATATTT
2447915 TTATATATTACGTATATATATTTTTTAAAATATCATATTAT
1 TTATATATTA--TAT-TATATTTTTT--AATATCATATT-T
2447956 TTATATACTT-TATTATAT
1 TTATATA-TTATATTATAT
2447974 AGGTGTATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
34 2 0.04
35 3 0.06
36 8 0.16
37 3 0.06
38 11 0.22
39 3 0.06
40 10 0.20
41 8 0.16
42 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (35 bp):
TTATATATTATATTATATTTTTTAATATCATATTT
Found at i:2447987 original size:21 final size:22
Alignment explanation
Indices: 2447957--2448012 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2447947 TCATATTATT
*
2447957 TATATACTTTAT-TATATA-GGTG
1 TATAT-CTTTATATATATATAG-G
2447979 TATATCTTTAATATATATATAGG
1 TATATCTTT-ATATATATATAGG
2448002 TATATCTTTAT
1 TATATCTTTAT
2448013 GTAATATTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 9 0.30
23 16 0.53
24 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (22 bp):
TATATCTTTATATATATATAGG
Found at i:2450057 original size:20 final size:22
Alignment explanation
Indices: 2450011--2450059 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
2450001 TGTAGCATAA
*
2450011 AATATATGTATTTAATTATTAT
1 AATATATGTAGTTAATTATTAT
*
2450033 -TTATAT-TAGTTAA-TATTAT
1 AATATATGTAGTTAATTATTAT
2450052 AATATATG
1 AATATATG
2450060 AGATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
AATATATGTAGTTAATTATTAT
Found at i:2454229 original size:20 final size:19
Alignment explanation
Indices: 2454206--2454264 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
2454196 AAAATCTAAA
2454206 ATTTTATAAATTCATAATTT
1 ATTTTATAAATT-ATAATTT
2454226 ATTTTATAAAATTATAAATTT
1 ATTTTAT-AAATTAT-AATTT
*
2454247 TTTTTA-AAATTTATAATT
1 ATTTTATAAA-TTATAATT
2454265 ATGCGAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 7 0.20
20 13 0.37
21 15 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATAAATTATAATTT
Found at i:2454245 original size:21 final size:21
Alignment explanation
Indices: 2454206--2454262 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
2454196 AAAATCTAAA
2454206 ATTTTAT-AAATTCAT-AATTT
1 ATTTTATAAAATT-ATAAATTT
2454226 ATTTTATAAAATTATAAATTT
1 ATTTTATAAAATTATAAATTT
2454247 -TTTT-TAAAATTTATAA
1 ATTTTATAAAA-TTATAA
2454263 TTATGCGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.15
20 19 0.56
21 10 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTATAAAATTATAAATTT
Found at i:2454606 original size:18 final size:17
Alignment explanation
Indices: 2454566--2454609 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2454556 ATTTTTTGCA
*
2454566 TTTTTTAAAATTTTAAC
1 TTTTTTATAATTTTAAC
**
2454583 GATTTTATAATTTTAAAC
1 TTTTTTATAATTTT-AAC
2454601 TTTTTTATA
1 TTTTTTATA
2454610 TAGATAACAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTTTATAATTTTAAC
Found at i:2455899 original size:18 final size:18
Alignment explanation
Indices: 2455876--2455912 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2455866 TTAATTCTAG
2455876 TTATTTGTAGTTATAATT
1 TTATTTGTAGTTATAATT
* *
2455894 TTATTTGTATTTGTAATT
1 TTATTTGTAGTTATAATT
2455912 T
1 T
2455913 ATAGACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (18 bp):
TTATTTGTAGTTATAATT
Found at i:2462512 original size:28 final size:28
Alignment explanation
Indices: 2462472--2462527 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2462462 GCAAAGGGTG
2462472 TTGCTAGTAAGCCTTATTTTCACTCTTT
1 TTGCTAGTAAGCCTTATTTTCACTCTTT
*
2462500 TTGCTAGTAAGCCTTATTTTCCCTCTTT
1 TTGCTAGTAAGCCTTATTTTCACTCTTT
2462528 CCTGTCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.50
Consensus pattern (28 bp):
TTGCTAGTAAGCCTTATTTTCACTCTTT
Found at i:2465909 original size:14 final size:12
Alignment explanation
Indices: 2465871--2465905 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2465861 TATAACCCTA
2465871 CATATATATATG
1 CATATATATATG
*
2465883 CACATATATATG
1 CATATATATATG
*
2465895 CATTTATATAT
1 CATATATATAT
2465906 ATGCCATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (12 bp):
CATATATATATG
Found at i:2466960 original size:21 final size:21
Alignment explanation
Indices: 2466927--2466968 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2466917 AACATTGGTT
* *
2466927 ATAATATACAAAAATTAATAA
1 ATAAGATACAAAAAATAATAA
*
2466948 ATAAGATATAAAAAATAATAA
1 ATAAGATACAAAAAATAATAA
2466969 TATATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
ATAAGATACAAAAAATAATAA
Found at i:2472730 original size:20 final size:20
Alignment explanation
Indices: 2472705--2472744 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2472695 TAACCCATTA
*
2472705 CTTACTCCCAGAGCCTTACT
1 CTTACTCCCACAGCCTTACT
*
2472725 CTTACTCCCACAGGCTTACT
1 CTTACTCCCACAGCCTTACT
2472745 TATTCTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.40, G:0.10, T:0.30
Consensus pattern (20 bp):
CTTACTCCCACAGCCTTACT
Found at i:2483982 original size:25 final size:25
Alignment explanation
Indices: 2483953--2484003 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2483943 CAAAGGAAAA
**
2483953 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
2483978 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
2484003 T
1 T
2484004 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:2487029 original size:3 final size:3
Alignment explanation
Indices: 2487021--2487052 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2487011 ACACCAACAT
2487021 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
2487053 ACAACAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:2489663 original size:4 final size:4
Alignment explanation
Indices: 2489654--2489678 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2489644 AATATAATGA
2489654 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
2489679 GGACTAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2491419 original size:21 final size:21
Alignment explanation
Indices: 2491389--2491429 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2491379 AAATAATTGA
* *
2491389 TAAATTCAAGCGATTTTTTCT
1 TAAATCCAAGCGATCTTTTCT
2491410 TAAATCCAAGCGATCTTTTC
1 TAAATCCAAGCGATCTTTTC
2491430 GTAGGCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAATCCAAGCGATCTTTTCT
Found at i:2492280 original size:38 final size:37
Alignment explanation
Indices: 2492225--2492299 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 37
2492215 CGATCATGGC
2492225 ATAGTCAAGTGGAACACCCCAAAGGCAAGGAAATATA
1 ATAGTCAAGTGGAACACCCCAAAGGCAAGGAAATATA
2492262 ATAGTCAAGCTGGAACACCCCAAAGGCAAGGAAATATA
1 ATAGTCAAG-TGGAACACCCCAAAGGCAAGGAAATATA
2492300 GGAAATCCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 9 0.24
38 28 0.76
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (37 bp):
ATAGTCAAGTGGAACACCCCAAAGGCAAGGAAATATA
Found at i:2494579 original size:46 final size:46
Alignment explanation
Indices: 2494529--2494704 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
2494519 TGGTTGAGCA
2494529 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2494575 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
2494620 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
2494668 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2494705 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2494685 original size:93 final size:93
Alignment explanation
Indices: 2494526--2494697 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
2494516 GGATGGTTGA
*
2494526 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
2494591 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2494619 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
2494683 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
2494698 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2509380 original size:39 final size:39
Alignment explanation
Indices: 2509329--2509573 Score: 393
Period size: 39 Copynumber: 6.3 Consensus size: 39
2509319 AACCCGAAAT
* *
2509329 TATATTAT-CAGCACAAAGCCTGCGGGACTTTAACCCGGA
1 TATATT-TCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
* *
2509368 TATATTTCCAGCACGAAGCCTGCGGGACTTTGGCCAGGA
1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
*
2509407 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCAGA
1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
*
2509446 TACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
*
2509485 TATATTTCCAGCACGAAGCCTGCGGGACTTTAACCCGGA
1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
* *
2509524 TACATTTCCAGCACGAAGCCTGCGGGACTTTGGCCCGGA
1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
2509563 TATATTTCCAG
1 TATATTTCCAG
2509574 TGTCTTGCAT
Statistics
Matches: 190, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 1 0.01
39 189 0.99
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
Found at i:2510513 original size:17 final size:18
Alignment explanation
Indices: 2510479--2510514 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2510469 AACACGAAAA
2510479 TTTTGAAACACGAGATTT
1 TTTTGAAACACGAGATTT
2510497 TTTTGAAACACGA-ATTT
1 TTTTGAAACACGAGATTT
2510514 T
1 T
2510515 CTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (18 bp):
TTTTGAAACACGAGATTT
Found at i:2510514 original size:16 final size:16
Alignment explanation
Indices: 2510468--2510514 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
2510458 TTTAAAAAAA
**
2510468 AAACACGAAAATTTTG
1 AAACACGAATTTTTTG
2510484 AAACACGAGATTTTTTTG
1 AAACACGA-A-TTTTTTG
2510502 AAACACGAATTTT
1 AAACACGAATTTT
2510515 CTTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
AAACACGAATTTTTTG
Found at i:2510538 original size:16 final size:16
Alignment explanation
Indices: 2510516--2510551 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2510506 ACGAATTTTC
*
2510516 TTTTTTAAACACGAAAA
1 TTTTTAAAACAC-AAAA
2510533 TTTTTAAAACACAAAA
1 TTTTTAAAACACAAAA
2510549 TTT
1 TTT
2510552 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTTTAAAACACAAAA
Found at i:2510564 original size:38 final size:37
Alignment explanation
Indices: 2510479--2510561 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
2510469 AACACGAAAA
** * * *
2510479 TTTTGAAACACGAGATTTTTTTGAAACACGAATTTTCT
1 TTTTGAAACACGA-AAATTTTTAAAACACAAAATTTCT
* *
2510517 TTTTTAAACACGAAAATTTTTAAAACACAAAATTTGT
1 TTTTGAAACACGAAAATTTTTAAAACACAAAATTTCT
2510554 TTTTGAAA
1 TTTTGAAA
2510562 ACATAAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
37 25 0.68
38 12 0.32
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTGAAACACGAAAATTTTTAAAACACAAAATTTCT
Found at i:2510573 original size:22 final size:20
Alignment explanation
Indices: 2510533--2510573 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2510523 AACACGAAAA
*
2510533 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
2510553 TTTTTGAAAACATAAAAATTT
1 TTTTT-AAAACA-AAAAATTT
2510574 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:2510619 original size:20 final size:20
Alignment explanation
Indices: 2510586--2510716 Score: 62
Period size: 21 Copynumber: 6.8 Consensus size: 20
2510576 ATAAAAAATG
**
2510586 AAACACGATGATTTTTTTTA
1 AAACACGAAAATTTTTTTTA
*
2510606 AAACACGAAAA---TTTAT-
1 AAACACGAAAATTTTTTTTA
* ** *
2510622 GAACACGGTCAATTTTTTTGA
1 AAACAC-GAAAATTTTTTTTA
* *
2510643 AAACATGAAAA---TTTTTG
1 AAACACGAAAATTTTTTTTA
* *
2510660 AAAGACGAGAATTTTTTTGTA
1 AAACACGAAAATTTTTTT-TA
2510681 AAACAC-AGAAATTTTTTTTGA
1 AAACACGA-AAATTTTTTTT-A
*
2510702 AAACAAGAAAATTTT
1 AAACACGAAAATTTT
2510717 CAAAATACGG
Statistics
Matches: 78, Mismatches: 21, Indels: 23
0.64 0.17 0.19
Matches are distributed among these distances:
16 5 0.06
17 19 0.24
20 21 0.27
21 32 0.41
22 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (20 bp):
AAACACGAAAATTTTTTTTA
Found at i:2510624 original size:37 final size:37
Alignment explanation
Indices: 2510583--2510691 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 37
2510573 TTGATAAAAA
2510583 ATGAAACACGATGATTTTTTTTAAAACACGAAAATTT
1 ATGAAACACGATGATTTTTTTTAAAACACGAAAATTT
* * * *
2510620 ATG-AACACGGTCAATTTTTTTGAAAACATGAAAATTT
1 ATGAAACACGAT-GATTTTTTTTAAAACACGAAAATTT
* *
2510657 TTGAAAGACGA-GAATTTTTTTGTAAAACACAGAAA
1 ATGAAACACGATG-ATTTTTTT-TAAAACAC-GAAA
2510692 TTTTTTTTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
36 7 0.12
37 35 0.61
38 11 0.19
39 4 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (37 bp):
ATGAAACACGATGATTTTTTTTAAAACACGAAAATTT
Found at i:2510658 original size:21 final size:19
Alignment explanation
Indices: 2510632--2510716 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 19
2510622 GAACACGGTC
2510632 AATTTTTTTGAAAACATGAA
1 AATTTTTTTGAAAACA-GAA
*
2510652 AA--TTTTTGAAAGAC-GAG
1 AATTTTTTTGAAA-ACAGAA
2510669 AATTTTTTTGTAAAACACAGAA
1 AATTTTTTTG--AAA-ACAGAA
*
2510691 ATTTTTTTTGAAAACAAGAA
1 AATTTTTTTGAAAAC-AGAA
2510711 AATTTT
1 AATTTT
2510717 CAAAATACGG
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
17 4 0.08
18 9 0.17
19 10 0.19
20 14 0.26
21 5 0.09
22 11 0.21
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.39
Consensus pattern (19 bp):
AATTTTTTTGAAAACAGAA
Found at i:2510704 original size:59 final size:51
Alignment explanation
Indices: 2510634--2510791 Score: 160
Period size: 59 Copynumber: 3.0 Consensus size: 51
2510624 ACACGGTCAA
2510634 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAATTTTTTTGTAAAACACAGAAAT
1 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAA--TTTTTG-AAAACAC-----T
* ** * *
2510693 TTTTTTTGAAAACAAGAAAATTTTCAAAATACGGGAATTTTTGAAAACACT
1 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAATTTTTGAAAACACT
*
2510744 TTTTTTT-AAAACATGAAAATTTTTGAAACACTG-GAA-TTTTGAAAACAC
1 TTTTTTTGAAAACATGAAAATTTTTGAAAGAC-GAGAATTTTTGAAAACAC
2510792 GAAGATTTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
49 12 0.13
50 23 0.26
51 9 0.10
56 7 0.08
57 6 0.07
59 32 0.36
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (51 bp):
TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAATTTTTGAAAACACT
Found at i:2510800 original size:34 final size:34
Alignment explanation
Indices: 2510745--2510835 Score: 114
Period size: 34 Copynumber: 2.6 Consensus size: 34
2510735 GAAAACACTT
* *
2510745 TTTTTTAAAACATGAAAATTTTTGAAACACTG-GAA
1 TTTTTGAAAACACG-AAATTTTTGAAAC-CTGAGAA
*
2510780 -TTTTGAAAACACGAAGATTTTTGAAACGTGAGAA
1 TTTTTGAAAACACGAA-ATTTTTGAAACCTGAGAA
2510814 TTTTTGAAAACACGAAATTTTT
1 TTTTTGAAAACACGAAATTTTT
2510836 AAAAAAAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 4 0.08
34 31 0.62
35 15 0.30
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (34 bp):
TTTTTGAAAACACGAAATTTTTGAAACCTGAGAA
Found at i:2510840 original size:17 final size:16
Alignment explanation
Indices: 2510746--2510839 Score: 80
Period size: 17 Copynumber: 5.6 Consensus size: 16
2510736 AAAACACTTT
*
2510746 TTTTTAAAACATGAAAA
1 TTTTTAAAACACG-AAA
* *
2510763 TTTTTGAAACACTGGAA
1 TTTTTAAAACAC-GAAA
*
2510780 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAA-A
* **
2510797 TTTTTGAAACGTGAGAA
1 TTTTTAAAACACGA-AA
2510814 TTTTTGAAAACACGAAA
1 TTTTT-AAAACACGAAA
2510831 TTTTTAAAA
1 TTTTTAAAA
2510840 AAAAACACGG
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
16 6 0.10
17 46 0.77
18 8 0.13
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.34
Consensus pattern (16 bp):
TTTTTAAAACACGAAA
Found at i:2510864 original size:17 final size:17
Alignment explanation
Indices: 2510746--2510874 Score: 65
Period size: 17 Copynumber: 7.3 Consensus size: 17
2510736 AAAACACTTT
* * *
2510746 TTTTTAAAACATGAAAA
1 TTTTTGAAACACGGAAA
2510763 TTTTTGAAACACTGG-AA
1 TTTTTGAAACAC-GGAAA
2510780 -TTTTGAAAACAC-GAAGA
1 TTTTTG-AAACACGGAA-A
2510797 TTTTTG-AA-ACGTGAGAA
1 TTTTTGAAACACG-GA-AA
2510814 TTTTTGAAAACAC-GAAA
1 TTTTTG-AAACACGGAAA
*
2510831 TTTTTAAAAAAAAACACGGAAA
1 TTTTT-----GAAACACGGAAA
2510853 TTTTTGAAACAC-GAGAA
1 TTTTTGAAACACGGA-AA
2510870 TTTTT
1 TTTTT
2510875 TTTAAAAAAC
Statistics
Matches: 89, Mismatches: 5, Indels: 36
0.68 0.04 0.28
Matches are distributed among these distances:
15 3 0.03
16 10 0.11
17 48 0.54
18 9 0.10
19 2 0.02
20 2 0.02
21 6 0.07
22 9 0.10
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:2510913 original size:39 final size:39
Alignment explanation
Indices: 2510812--2510905 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
2510802 GAAACGTGAG
*** *
2510812 AATTTTTGAAAACACGA-AATTTTTAAAAAAAAACACGGA
1 AATTTTTG-AAACACGAGAATTTTTTTTAAAAAACACGAA
*
2510851 AATTTTTGAAACACGAGAATTTTTTTTAAAAAACCCGAA
1 AATTTTTGAAACACGAGAATTTTTTTTAAAAAACACGAA
2510890 AATTTTTGAAACACGA
1 AATTTTTGAAACACGA
2510906 TTTTTTTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
38 8 0.16
39 41 0.84
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.30
Consensus pattern (39 bp):
AATTTTTGAAACACGAGAATTTTTTTTAAAAAACACGAA
Found at i:2511347 original size:21 final size:21
Alignment explanation
Indices: 2511321--2511360 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2511311 AAAAAGCTCA
2511321 AAAATACGAGATTGACCGATC
1 AAAATACGAGATTGACCGATC
*
2511342 AAAATACGAGCTTGACCGA
1 AAAATACGAGATTGACCGA
2511361 GAGGGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAATACGAGATTGACCGATC
Found at i:2511409 original size:21 final size:21
Alignment explanation
Indices: 2511386--2511465 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
2511376 CGAGCCTTCT
*
2511386 TTTTTTCTTTTTTCT-TTTCC
1 TTTTTTCTTTTTTCTCTTTTC
2511406 TTTTTTCCCTTTTTTTTCTCTTTTC
1 TTTTTT--C--TTTTTTCTCTTTTC
*
2511431 TTTTTTCTTTTTTCTGTTTTC
1 TTTTTTCTTTTTTCTCTTTTC
*
2511452 TGTTTTCTTTTTTC
1 TTTTTTCTTTTTTC
2511466 CTTCTTTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.12
21 26 0.50
22 1 0.02
23 1 0.02
24 8 0.15
25 10 0.19
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTTTTTCTCTTTTC
Found at i:2511416 original size:9 final size:8
Alignment explanation
Indices: 2511384--2511479 Score: 55
Period size: 7 Copynumber: 12.5 Consensus size: 8
2511374 CTCGAGCCTT
*
2511384 CTTTTTTT
1 CTTTTTTC
2511392 CTTTTTT-
1 CTTTTTTC
2511399 C--TTTTC
1 CTTTTTTC
2511405 CTTTTTTCC
1 CTTTTTT-C
*
2511414 CTTTTTTTT
1 C-TTTTTTC
*
2511423 CTCTTTT-
1 CTTTTTTC
2511430 CTTTTTT-
1 CTTTTTTC
2511437 CTTTTTT-
1 CTTTTTTC
*
2511444 CTGTTTT-
1 CTTTTTTC
*
2511451 CTGTTTT-
1 CTTTTTTC
2511458 CTTTTTTC
1 CTTTTTTC
2511466 CTTCTTTTTC
1 C-T-TTTTTC
2511476 CTTT
1 CTTT
2511480 GGCCTGCTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
5 4 0.05
6 1 0.01
7 33 0.44
8 19 0.25
9 5 0.07
10 13 0.17
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (8 bp):
CTTTTTTC
Found at i:2511423 original size:31 final size:32
Alignment explanation
Indices: 2511385--2511444 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
2511375 TCGAGCCTTC
*
2511385 TTTTTTTCTTTTTTC-TTTTCCTTTTTTCCCT
1 TTTTTTTCTCTTTTCTTTTTCCTTTTTTCCCT
*
2511416 TTTTTTTCTCTTTTCTTTTTTCTTTTTTC
1 TTTTTTTCTCTTTTCTTTTTCCTTTTTTC
2511445 TGTTTTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (32 bp):
TTTTTTTCTCTTTTCTTTTTCCTTTTTTCCCT
Found at i:2511428 original size:33 final size:32
Alignment explanation
Indices: 2511380--2511444 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
2511370 ACGACTCGAG
2511380 CCTTCTTTTTTTCTTTT-TTCTTTTCCTTTTTTC
1 CCTTCTTTTTTTCTTTTCTT-TTTT-CTTTTTTC
2511413 CCTT-TTTTTTCTCTTTTCTTTTTTCTTTTTTC
1 CCTTCTTTTTT-TCTTTTCTTTTTTCTTTTTTC
2511445 TGTTTTCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (32 bp):
CCTTCTTTTTTTCTTTTCTTTTTTCTTTTTTC
Found at i:2511479 original size:7 final size:7
Alignment explanation
Indices: 2511386--2511465 Score: 81
Period size: 7 Copynumber: 11.0 Consensus size: 7
2511376 CGAGCCTTCT
2511386 TTTTTTC
1 TTTTTTC
2511393 TTTTTTC
1 TTTTTTC
*
2511400 -TTTTCC
1 TTTTTTC
2511406 TTTTTTCCC
1 TTTTTT--C
2511415 TTTTTTTTC
1 --TTTTTTC
*
2511424 TCTTTTC
1 TTTTTTC
2511431 TTTTTTC
1 TTTTTTC
2511438 TTTTTTC
1 TTTTTTC
*
2511445 TGTTTTC
1 TTTTTTC
*
2511452 TGTTTTC
1 TTTTTTC
2511459 TTTTTTC
1 TTTTTTC
2511466 CTTCTTTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
6 5 0.08
7 49 0.79
9 2 0.03
11 6 0.10
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:2511784 original size:18 final size:18
Alignment explanation
Indices: 2511744--2511787 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2511734 CCTAGCCGCC
2511744 GCGCCG-CGCCGTCGCTT
1 GCGCCGTCGCCGTCGCTT
*
2511761 GTGCCGTCGCCGTCGTCTT
1 GCGCCGTCGCCGTCG-CTT
2511780 -CGCCGTCG
1 GCGCCGTCG
2511788 AGCCGCTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 3 0.13
ACGTcount: A:0.00, C:0.43, G:0.34, T:0.23
Consensus pattern (18 bp):
GCGCCGTCGCCGTCGCTT
Found at i:2511863 original size:20 final size:20
Alignment explanation
Indices: 2511806--2511863 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2511796 TCGGAGGCTC
*
2511806 TCCTCTTC-TTCTC-CTTTC
1 TCCTCTTCTTTCTCTCTTTT
*
2511824 TCCTC-TCTTTCTCTCCTTT
1 TCCTCTTCTTTCTCTCTTTT
*
2511843 TCCTCTTCTTTTTCTCTTTT
1 TCCTCTTCTTTCTCTCTTTT
2511863 T
1 T
2511864 TGCAAGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 10 0.30
19 8 0.24
20 13 0.39
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TCCTCTTCTTTCTCTCTTTT
Found at i:2512121 original size:29 final size:29
Alignment explanation
Indices: 2512088--2512204 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
2512078 TGTAATTTTT
*
2512088 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
2512117 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
2512147 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
2512176 GGAAAAGTTTAGGTGTCAAAATGCAATTT
1 AGAAAA-TTTAGG-GTTAAAATGAAATTT
2512205 TTATTTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 16 0.22
30 54 0.75
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:2512143 original size:30 final size:30
Alignment explanation
Indices: 2512103--2512204 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2512093 ATTTAGGATT
*
2512103 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
2512133 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
2512163 AAAATGAAATTT-AGGAAAAGTTTAGGTGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
2512193 AAAATGCAATTT
1 AAAATGAAATTT
2512205 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:2513288 original size:49 final size:49
Alignment explanation
Indices: 2513235--2513331 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
2513225 ATCGCTATAG
2513235 ATTTTTAATTAGTAAATGGCTTAAGGACTTAAATTGCAATTAACCCAAT
1 ATTTTTAATTAGTAAATGGCTTAAGGACTTAAATTGCAATTAACCCAAT
*
2513284 ATTTTTAATTAGTAAATGGCTTAAGGACTTAAATTGTAATTAACCCAA
1 ATTTTTAATTAGTAAATGGCTTAAGGACTTAAATTGCAATTAACCCAA
2513332 GGTTCAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (49 bp):
ATTTTTAATTAGTAAATGGCTTAAGGACTTAAATTGCAATTAACCCAAT
Found at i:2514074 original size:316 final size:316
Alignment explanation
Indices: 2513501--2514177 Score: 1345
Period size: 316 Copynumber: 2.1 Consensus size: 316
2513491 CTTGTAATTT
2513501 TATAATATATGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTCGAACCTGTACATATTTTTAT
1 TATAATATATGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTCGAACCTGTACATATTTTTAT
2513566 TAAATTTGAATAAAAATATTTATGGAGTTGTTTTATAAGTGAATTGAATTTTGGACAAGTAATTT
66 TAAATTTGAATAAAAATATTTATGGAGTTGTTTTATAAGTGAATTGAATTTTGGACAAGTAATTT
2513631 AGCCGTATTAGGGCTTAATTGAGGTCCAGGGACTAAATCGTAAAGTTTAATCGCTATAGATTTTT
131 AGCCGTATTAGGGCTTAATTGAGGTCCAGGGACTAAATCGTAAAGTTTAATCGCTATAGATTTTT
2513696 AATTAGTAAATGGCTTAAGGACTTAAATTGTAATTAACCCAAGGTTCAAAATAGAAATTATACCA
196 AATTAGTAAATGGCTTAAGGACTTAAATTGTAATTAACCCAAGGTTCAAAATAGAAATTATACCA
2513761 TGTTAAATTTCATGTAAGTGGATGGTATAATTATATAATTAATAATTTAAACTTAA
261 TGTTAAATTTCATGTAAGTGGATGGTATAATTATATAATTAATAATTTAAACTTAA
*
2513817 TATAATATACGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTCGAACCTGTACATATTTTTAT
1 TATAATATATGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTCGAACCTGTACATATTTTTAT
2513882 TAAATTTGAATAAAAATATTTATGGAGTTGTTTTATAAGTGAATTGAATTTTGGACAAGTAATTT
66 TAAATTTGAATAAAAATATTTATGGAGTTGTTTTATAAGTGAATTGAATTTTGGACAAGTAATTT
2513947 AGCCGTATTAGGGCTTAATTGAGGTCCAGGGACTAAATCGTAAAGTTTAATCGCTATAGATTTTT
131 AGCCGTATTAGGGCTTAATTGAGGTCCAGGGACTAAATCGTAAAGTTTAATCGCTATAGATTTTT
2514012 AATTAGTAAATGGCTTAAGGACTTAAATTGTAATTAACCCAAGGTTCAAAATAGAAATTATACCA
196 AATTAGTAAATGGCTTAAGGACTTAAATTGTAATTAACCCAAGGTTCAAAATAGAAATTATACCA
2514077 TGTTAAATTTCATGTAAGTGGATGGTATAATTATATAATTAATAATTTAAACTTAA
261 TGTTAAATTTCATGTAAGTGGATGGTATAATTATATAATTAATAATTTAAACTTAA
2514133 TATAATATATGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTC
1 TATAATATATGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTC
2514178 AATCCATAAA
Statistics
Matches: 359, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
316 359 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (316 bp):
TATAATATATGCATGTTCGGTGGGAAGGGAGAGAAATACATCTTCGAACCTGTACATATTTTTAT
TAAATTTGAATAAAAATATTTATGGAGTTGTTTTATAAGTGAATTGAATTTTGGACAAGTAATTT
AGCCGTATTAGGGCTTAATTGAGGTCCAGGGACTAAATCGTAAAGTTTAATCGCTATAGATTTTT
AATTAGTAAATGGCTTAAGGACTTAAATTGTAATTAACCCAAGGTTCAAAATAGAAATTATACCA
TGTTAAATTTCATGTAAGTGGATGGTATAATTATATAATTAATAATTTAAACTTAA
Found at i:2515666 original size:30 final size:30
Alignment explanation
Indices: 2515632--2515689 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2515622 CTGACAAGAA
2515632 CATAGTGCATCATTAATTATCCCTTTGTAT
1 CATAGTGCATCATTAATTATCCCTTTGTAT
2515662 CATAGTGCATCATTAATTATCCCTTTGT
1 CATAGTGCATCATTAATTATCCCTTTGT
2515690 GTCTTTGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (30 bp):
CATAGTGCATCATTAATTATCCCTTTGTAT
Found at i:2517275 original size:3 final size:3
Alignment explanation
Indices: 2517267--2517297 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2517257 TCACTTCTAG
2517267 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2517298 GTCACTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2517405 original size:20 final size:20
Alignment explanation
Indices: 2517380--2517418 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2517370 CTAATATGAC
*
2517380 AAATTTCTAAATGTCACAAT
1 AAATTTCTAAATATCACAAT
2517400 AAATTTCTAAATATCACAA
1 AAATTTCTAAATATCACAA
2517419 AAGTTTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (20 bp):
AAATTTCTAAATATCACAAT
Found at i:2520946 original size:7 final size:7
Alignment explanation
Indices: 2520934--2520977 Score: 70
Period size: 7 Copynumber: 6.1 Consensus size: 7
2520924 AGCCCAAAAN
2520934 AAATTAA
1 AAATTAA
2520941 AAATTAA
1 AAATTAA
2520948 AAATTAA
1 AAATTAA
2520955 AAATTAA
1 AAATTAA
2520962 AAATTTAA
1 AAA-TTAA
*
2520970 AGATTAA
1 AAATTAA
2520977 A
1 A
2520978 TTTCAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (7 bp):
AAATTAA
Found at i:2523260 original size:25 final size:25
Alignment explanation
Indices: 2523208--2523311 Score: 66
Period size: 25 Copynumber: 4.1 Consensus size: 25
2523198 GCTTTATAGG
* * *
2523208 TAACCTACCACAAAGACGTTACAGA
1 TAACCTACCACAAAGGCTTTACAAA
* *
2523233 TAACCTGCCACAAAGGCTTTCCAAA
1 TAACCTACCACAAAGGCTTTACAAA
** * *
2523258 TAAATTACCACAAAAG-TTGTACAGA
1 TAACCTACCACAAAGGCTT-TACAAA
* * * *
2523283 TGACTTGCCACAAAGGCTTTCCCAAA
1 TAACCTACCACAAAGGCTTT-ACAAA
2523309 TAA
1 TAA
2523312 ATCACCATAA
Statistics
Matches: 58, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
24 2 0.03
25 49 0.84
26 7 0.12
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (25 bp):
TAACCTACCACAAAGGCTTTACAAA
Found at i:2523271 original size:50 final size:52
Alignment explanation
Indices: 2523213--2523323 Score: 149
Period size: 50 Copynumber: 2.2 Consensus size: 52
2523203 ATAGGTAACC
2523213 TACCACAAAGACG-T-TACAGATAACCTGCCACAAAGGCTTT-CCAAATAAAT
1 TACCACAAAGA-GTTGTACAGATAACCTGCCACAAAGGCTTTCCCAAATAAAT
* *
2523263 TACCACAAA-AGTTGTACAGATGACTTGCCACAAAGGCTTTCCCAAATAAAT
1 TACCACAAAGAGTTGTACAGATAACCTGCCACAAAGGCTTTCCCAAATAAAT
* *
2523314 CACCATAAAG
1 TACCACAAAG
2523324 GCTTCCCCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
48 1 0.02
49 2 0.04
50 33 0.62
51 17 0.32
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.21
Consensus pattern (52 bp):
TACCACAAAGAGTTGTACAGATAACCTGCCACAAAGGCTTTCCCAAATAAAT
Found at i:2523332 original size:26 final size:26
Alignment explanation
Indices: 2523294--2523350 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
2523284 GACTTGCCAC
* *
2523294 AAAGGCTTTCCCAAATAAATCACCAT
1 AAAGGCTTCCCCAAATAAATAACCAT
2523320 AAAGGCTTCCCCAAATAAATAACCAT
1 AAAGGCTTCCCCAAATAAATAACCAT
2523346 AAAGG
1 AAAGG
2523351 ATTTACAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.19
Consensus pattern (26 bp):
AAAGGCTTCCCCAAATAAATAACCAT
Found at i:2523335 original size:77 final size:76
Alignment explanation
Indices: 2523240--2523415 Score: 203
Period size: 77 Copynumber: 2.3 Consensus size: 76
2523230 AGATAACCTG
* * * *
2523240 CCACAAAGGCTTTCCAAATAAATTACCACAAAAG-TTGTACAGATGACTTGCCACAAAGGCTTTC
1 CCACAAAGGCTTCCCAAATAAATAACCACAAAAGATT-TACAGATGACTCGACACAAAGGC-TTC
2523304 CC-AAATAAATCA
64 CCTAAATAAATCA
* * * * *
2523316 CCATAAAGGCTTCCCCAAATAAATAACCATAAAGGATTTACAGGTGACTCGACACAGAGGCTTCC
1 CCACAAAGGCTT-CCCAAATAAATAACCACAAAAGATTTACAGATGACTCGACACAAAGGCTTCC
2523381 CTAAATAAATCA
65 CTAAATAAATCA
* * *
2523393 TCACAAAGTCTTCTCAAATAAAT
1 CCACAAAGGCTTCCCAAATAAAT
2523416 CCCTATAAAG
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
76 26 0.31
77 56 0.67
78 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (76 bp):
CCACAAAGGCTTCCCAAATAAATAACCACAAAAGATTTACAGATGACTCGACACAAAGGCTTCCC
TAAATAAATCA
Found at i:2526288 original size:21 final size:20
Alignment explanation
Indices: 2526264--2526327 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
2526254 CGAGCCCAAT
2526264 TTACAA-ACAAATAAAAATAAA
1 TTACAACACAAAT-AAAA-AAA
*
2526285 TTACAAGCCCAAATAAAAAAA
1 TTACAA-CACAAATAAAAAAA
*
2526306 TTACAAGCCCAAATAAATAAAA
1 TTACAA-CACAAATAAA-AAAA
2526328 GAAACCTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
21 26 0.67
22 8 0.21
23 5 0.13
ACGTcount: A:0.64, C:0.16, G:0.03, T:0.17
Consensus pattern (20 bp):
TTACAACACAAATAAAAAAA
Found at i:2537555 original size:17 final size:16
Alignment explanation
Indices: 2537530--2537571 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
2537520 TTGTTTTTTG
2537530 AAAAATATTT-ATTAAT
1 AAAAATATTTAATT-AT
2537546 AAAAAGTATTTAATTAT
1 AAAAA-TATTTAATTAT
2537563 AAAATATAT
1 AAAA-ATAT
2537572 AAATTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAAATATTTAATTAT
Found at i:2547056 original size:303 final size:303
Alignment explanation
Indices: 2546509--2547118 Score: 1175
Period size: 303 Copynumber: 2.0 Consensus size: 303
2546499 GTTGGTAGTG
2546509 TGGAAAAAGTTCTGGGTTCGATCCAGGGCTTTAGTAAAATTTTGCATTTTTTTTAAAATACCCTG
1 TGGAAAAAGTTCTGGGTTCGATCCAGGGCTTTAGTAAAATTTTGCATTTTTTTTAAAATACCCTG
2546574 AGCATTAGGTGGAAGGCTTATTAATAAGGCCTGGTAAAATTTAACACAAGGTAATGCTTGGCTTA
66 AGCATTAGGTGGAAGGCTTATTAATAAGGCCTGGTAAAATTTAACACAAGGTAATGCTTGGCTTA
* *
2546639 GTGGCAAAAGGCGTTGGTAGCAAGCAGGAAGTCCAGGGTTCAAGTCTTGGCCTTGGCGAAAATTT
131 GTGGCAAAAGGCGTTGGTAGCAAGCAGGAAGTCCAGGGTTAAAGTCCTGGCCTTGGCGAAAATTT
2546704 TTATTGCGCATATAATTAGTAGGGAAGCTAGCATTTAGGCCTTATAAATATGTTTGGTGGAAATA
196 TTATTGCGCATATAATTAGTAGGGAAGCTAGCATTTAGGCCTTATAAATATGTTTGGTGGAAATA
2546769 TGACATAAGAGTGCCTAGGGGGGCAGTGGCGAGAAGCATACTA
261 TGACATAAGAGTGCCTAGGGGGGCAGTGGCGAGAAGCATACTA
2546812 TGGAAAAAGTTCTGGGTTCGATCCAGGGCTTTAGTAAAATTTTGCATTTTTTTTAAAATACCCTG
1 TGGAAAAAGTTCTGGGTTCGATCCAGGGCTTTAGTAAAATTTTGCATTTTTTTTAAAATACCCTG
2546877 AGCATTAGGTGGAAGGCTTATTAATAAGGCCTGGTAAAATTTAACACAAGGTAATGCTTGGCTTA
66 AGCATTAGGTGGAAGGCTTATTAATAAGGCCTGGTAAAATTTAACACAAGGTAATGCTTGGCTTA
2546942 GTGGCAAAAGGCGTTGGTAGCAAGCAGGAAGTCCAGGGTTAAAGTCCTGGCCTTGGCGAAAATTT
131 GTGGCAAAAGGCGTTGGTAGCAAGCAGGAAGTCCAGGGTTAAAGTCCTGGCCTTGGCGAAAATTT
*
2547007 TTATTGTGCATATAATTAGTAGGGAAGCTAGCATTTAGGCCTTATAAATATGTTTGGTGGAAATA
196 TTATTGCGCATATAATTAGTAGGGAAGCTAGCATTTAGGCCTTATAAATATGTTTGGTGGAAATA
* *
2547072 TGGCATAAGAGTGCCTAGGGGGGCAGTGGCGAGAAGCATGCTA
261 TGACATAAGAGTGCCTAGGGGGGCAGTGGCGAGAAGCATACTA
2547115 TGGA
1 TGGA
2547119 TTTGAGAGGT
Statistics
Matches: 302, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
303 302 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (303 bp):
TGGAAAAAGTTCTGGGTTCGATCCAGGGCTTTAGTAAAATTTTGCATTTTTTTTAAAATACCCTG
AGCATTAGGTGGAAGGCTTATTAATAAGGCCTGGTAAAATTTAACACAAGGTAATGCTTGGCTTA
GTGGCAAAAGGCGTTGGTAGCAAGCAGGAAGTCCAGGGTTAAAGTCCTGGCCTTGGCGAAAATTT
TTATTGCGCATATAATTAGTAGGGAAGCTAGCATTTAGGCCTTATAAATATGTTTGGTGGAAATA
TGACATAAGAGTGCCTAGGGGGGCAGTGGCGAGAAGCATACTA
Found at i:2548337 original size:42 final size:42
Alignment explanation
Indices: 2548290--2548384 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
2548280 TCCAGGTGAT
*
2548290 AAGGTGTGTACTTCTACCCTATGATAGCTTGATATAAAGCCG
1 AAGGTGTGTACTTCTACCCTATGATAGCTTGATATAAAGCAG
2548332 AAGGTGTGTACTTCTACCCTATGATAGCTTGATATAAAGCAG
1 AAGGTGTGTACTTCTACCCTATGATAGCTTGATATAAAGCAG
2548374 AAGGTGTGTAC
1 AAGGTGTGTAC
2548385 ATACACTACA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (42 bp):
AAGGTGTGTACTTCTACCCTATGATAGCTTGATATAAAGCAG
Found at i:2548728 original size:28 final size:29
Alignment explanation
Indices: 2548669--2548733 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
2548659 GGCCGGATGA
* *
2548669 GCCATATGAATGTGATTTGGGCCTAATAG
1 GCCATATGAATGAGATTTAGGCCTAATAG
* *
2548698 GCCATATGAATGAGA-TTAGGCCTAGTGG
1 GCCATATGAATGAGATTTAGGCCTAATAG
2548726 GCCATATG
1 GCCATATG
2548734 CATGTATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (29 bp):
GCCATATGAATGAGATTTAGGCCTAATAG
Found at i:2548745 original size:28 final size:27
Alignment explanation
Indices: 2548669--2548746 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
2548659 GGCCGGATGA
*
2548669 GCCATATGAATGTGATTTGGGCCTAATAG
1 GCCATATGAATGT-A-TTAGGCCTAATAG
* * *
2548698 GCCATATGAATGAGATTAGGCCTAGTGG
1 GCCATATGAATG-TATTAGGCCTAATAG
*
2548726 GCCATATGCATGTATGTAGGC
1 GCCATATGAATGTAT-TAGGC
2548747 TTGTTTGGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 2 0.05
28 26 0.63
29 13 0.32
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (27 bp):
GCCATATGAATGTATTAGGCCTAATAG
Found at i:2550638 original size:34 final size:33
Alignment explanation
Indices: 2550595--2550704 Score: 132
Period size: 34 Copynumber: 3.2 Consensus size: 33
2550585 AAGTGTCTCT
2550595 CATGTGTGGGAGCAAGACCCTCGTAAGCCTTCCC
1 CATGTGTGGGAGCAAGACCCT-GTAAGCCTTCCC
* *
2550629 CATGTGTGGGAGTAGGACTCCTGTAAG-CTTCCCC
1 CATGTGTGGGAGCAAGAC-CCTGTAAGCCTT-CCC
*
2550663 CATGTGTGGGAGCAAGACCCCTTGTAAGCTTTCCTC
1 CATGTGTGGGAGCAAGA-CCC-TGTAAGCCTTCC-C
2550699 CATGTG
1 CATGTG
2550705 CAGGAACAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
33 3 0.05
34 41 0.63
35 12 0.18
36 9 0.14
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.25
Consensus pattern (33 bp):
CATGTGTGGGAGCAAGACCCTGTAAGCCTTCCC
Found at i:2554899 original size:18 final size:16
Alignment explanation
Indices: 2554870--2554915 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
2554860 ATTTTCTTTC
*
2554870 CTTTTCCTTTCTATTT
1 CTTTTTCTTTCTATTT
2554886 CGTTTGTTCTTTCTATTT
1 C-TTT-TTCTTTCTATTT
2554904 CTTTTTCTTTCT
1 CTTTTTCTTTCT
2554916 TTATTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (16 bp):
CTTTTTCTTTCTATTT
Found at i:2554920 original size:18 final size:18
Alignment explanation
Indices: 2554876--2554915 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2554866 TTTCCTTTTC
2554876 CTTTCTATTTCGTTTGTT
1 CTTTCTATTTCGTTTGTT
2554894 CTTTCTATTTC-TTT-TT
1 CTTTCTATTTCGTTTGTT
2554910 CTTTCT
1 CTTTCT
2554916 TTATTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.70
Consensus pattern (18 bp):
CTTTCTATTTCGTTTGTT
Found at i:2558293 original size:14 final size:14
Alignment explanation
Indices: 2558254--2558293 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
2558244 TAACTTTTAA
2558254 TTATTATTTAAATT
1 TTATTATTTAAATT
**
2558268 TATACAATTTAAATT
1 T-TATTATTTAAATT
2558283 TTATTATTTAA
1 TTATTATTTAA
2558294 TATAGACATG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATTTAAATT
Found at i:2563191 original size:28 final size:28
Alignment explanation
Indices: 2563159--2563214 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2563149 GAGAAGTAAG
2563159 CCTCAAATGAACAGTTGGCGAAGAGGGT
1 CCTCAAATGAACAGTTGGCGAAGAGGGT
* *
2563187 CCTCAAATGAATAGTTGGTGAAGAGGGT
1 CCTCAAATGAACAGTTGGCGAAGAGGGT
2563215 TCGCTGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.21
Consensus pattern (28 bp):
CCTCAAATGAACAGTTGGCGAAGAGGGT
Found at i:2565372 original size:27 final size:27
Alignment explanation
Indices: 2565334--2565387 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2565324 ATAAAAGAAT
2565334 TATGCGCTTTAACGCACTCAAATCCAC
1 TATGCGCTTTAACGCACTCAAATCCAC
*
2565361 TATGCGCTTTAATGCACTCAAATCCAC
1 TATGCGCTTTAACGCACTCAAATCCAC
2565388 ATCTTCTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.31, G:0.11, T:0.28
Consensus pattern (27 bp):
TATGCGCTTTAACGCACTCAAATCCAC
Found at i:2568502 original size:18 final size:18
Alignment explanation
Indices: 2568479--2568513 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2568469 GCTAAATTTG
2568479 TTCCAGGTATC-TCAATTA
1 TTCCAGGT-TCATCAATTA
2568497 TTCCAGGTTCATCAATT
1 TTCCAGGTTCATCAATT
2568514 TTTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (18 bp):
TTCCAGGTTCATCAATTA
Found at i:2573375 original size:23 final size:22
Alignment explanation
Indices: 2573345--2573389 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2573335 AAATTAAATC
*
2573345 TCTAAGATTTCAAAATCATATCT
1 TCTAAGATTGC-AAATCATATCT
*
2573368 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCAAATCATATCT
2573390 AAGATTGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (22 bp):
TCTAAGATTGCAAATCATATCT
Found at i:2573420 original size:35 final size:36
Alignment explanation
Indices: 2573368--2573493 Score: 175
Period size: 35 Copynumber: 3.5 Consensus size: 36
2573358 AATCATATCT
*
2573368 TCTAAGATTGCATATCATATCTAAGATTGCAATTATA
1 TCTAAGATTGC-TATCATATCTAAGATTGCAATCATA
*
2573405 TCTAAGCTTG-TATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGCA-ATCATA
* *
2573441 TCTAAGATTGCAATCATATCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGCAATCATA
2573476 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
2573494 TGAAGATTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
35 36 0.45
36 19 0.24
37 25 0.31
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (36 bp):
TCTAAGATTGCTATCATATCTAAGATTGCAATCATA
Found at i:2573429 original size:54 final size:54
Alignment explanation
Indices: 2573368--2573493 Score: 234
Period size: 54 Copynumber: 2.3 Consensus size: 54
2573358 AATCATATCT
* *
2573368 TCTAAGATTGCATATCATATCTAAGATTGCAATTATATCTAAGCTTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
2573422 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
2573476 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
2573494 TGAAGATTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
Found at i:2573501 original size:17 final size:19
Alignment explanation
Indices: 2573368--2573493 Score: 192
Period size: 19 Copynumber: 6.9 Consensus size: 19
2573358 AATCATATCT
2573368 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2573387 TCTAAGATTGCA-ATTATA
1 TCTAAGATTGCATATCATA
*
2573405 TCTAAGCTTG--TATCATA
1 TCTAAGATTGCATATCATA
2573422 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2573441 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
2573459 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
2573476 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
2573494 TGAAGATTAT
Statistics
Matches: 97, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
17 30 0.31
18 30 0.31
19 37 0.38
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2575924 original size:26 final size:26
Alignment explanation
Indices: 2575863--2575982 Score: 100
Period size: 26 Copynumber: 4.5 Consensus size: 26
2575853 CGAAAGTTTG
**
2575863 AAATAAATAATATACAGAAA-AAGTTTA
1 AAATAAATAATATGTA-AAATAA-TTTA
*
2575890 AAATGAATAATATGTAAAATAATTTA
1 AAATAAATAATATGTAAAATAATTTA
* * *
2575916 AGATAAATAATATAT-AAATGAGTTTA
1 AAATAAATAATATGTAAAAT-AATTTA
** *
2575942 AAATAAATGTTATGTAAAAAGAAATTTA
1 AAATAAATAATATGT-AAAA-TAATTTA
2575970 AAATAAATAATAT
1 AAATAAATAATAT
2575983 ACAAGACATT
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
25 4 0.05
26 35 0.48
27 15 0.21
28 19 0.26
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (26 bp):
AAATAAATAATATGTAAAATAATTTA
Found at i:2575956 original size:52 final size:55
Alignment explanation
Indices: 2575854--2575985 Score: 153
Period size: 54 Copynumber: 2.4 Consensus size: 55
2575844 TAATATAGGC
* *
2575854 GAAAGTTTGAAATAAATAATATACAGAAAAAGTTTAAAATGAATAATATGT-AAAA
1 GAAA-TTTAAAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAA
* * * ** **
2575909 -TAATTTAAGATAAATAATATATA-AATGAGTTTAAAATAAATGTTATGTAAAAA
1 GAAATTTAAAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAA
2575962 GAAATTTAAAATAAATAATATACA
1 GAAATTTAAAATAAATAATATACA
2575986 AGACATTTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
52 20 0.32
53 21 0.33
54 22 0.35
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (55 bp):
GAAATTTAAAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAA
Found at i:2577374 original size:15 final size:16
Alignment explanation
Indices: 2577354--2577383 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2577344 CGGAGGTACG
2577354 TTTTATTATT-TTTCT
1 TTTTATTATTATTTCT
2577369 TTTTATTATTATTTC
1 TTTTATTATTATTTC
2577384 GTGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTATTATTTCT
Found at i:2578489 original size:43 final size:43
Alignment explanation
Indices: 2578433--2578720 Score: 190
Period size: 43 Copynumber: 6.7 Consensus size: 43
2578423 CGCCTTCGAT
* *
2578433 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTGAATTCAAC
1 CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTGAATTCAAC
* * **
2578476 CTGTTACCCTACTGCTAAGGG-GTTTAA-AGTCTGTAAATTCGGC
1 CTGTTACCCTACTGCTTAGGGTG-TTAAGA-TCTGTGAATTCAAC
* * * ** * * * *
2578519 TTGTTACCCTACTGCTTAGGGGGTTAA-AGCCCATCACCTTCGAT
1 CTGTTACCCTACTGCTTAGGGTGTTAAGA-TCTGTGA-ATTCAAC
* * * * *
2578563 CTGTTTCCCTACTGCTTAGGGTGTTAAGATTTGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTGAATTCAAC
* ** ** ** *
2578606 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCT-TCGTCTTTGAT
1 CTGTTACCCTACTGCTTAGGGTGTTAA-GATCTGT-GAATTCAAC
* * * *
2578650 CTATTTCCTTACTGCTTAGGGTGATAAGATCTGTGAATTCAAC
1 CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTGAATTCAAC
2578693 CTGTTACCCTACTGCTTAGGAGT-TTAAG
1 CTGTTACCCTACTGCTTAGG-GTGTTAAG
2578721 TACTGCTTAG
Statistics
Matches: 181, Mismatches: 55, Indels: 18
0.71 0.22 0.07
Matches are distributed among these distances:
42 2 0.01
43 117 0.65
44 61 0.34
45 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTGAATTCAAC
Found at i:2578567 original size:87 final size:87
Alignment explanation
Indices: 2578476--2578712 Score: 282
Period size: 87 Copynumber: 2.7 Consensus size: 87
2578466 TGAATTCAAC
* * * *
2578476 CTGTTACCCTACTGCTAAGGGGTTTAAAG-TCTGTAAATTCGGCTTGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTA-GGGTTTAAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
2578540 GGTTAAAGCCCATCACCTTCGAT
65 GGTTAAAGCCCATCACCTTCGAT
* *
2578563 CTGTTTCCCTACTGCTTAGGGTGTT-AAGATTTGTAAATTTAGCCTGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGGT-TTAAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
* * ** *
2578627 GGTTAAGGCCCTTCGTCTTTGAT
65 GGTTAAAGCCCATCACCTTCGAT
* * * * *
2578650 CTATTTCCTTACTGCTTAGGG-TGATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGTTTA-AAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGG
2578713 AGTTTAAGTA
Statistics
Matches: 128, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
85 1 0.01
86 7 0.05
87 120 0.94
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (87 bp):
CTGTTTCCCTACTGCTTAGGGTTTAAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
GTTAAAGCCCATCACCTTCGAT
Found at i:2578627 original size:130 final size:130
Alignment explanation
Indices: 2578390--2578632 Score: 387
Period size: 130 Copynumber: 1.9 Consensus size: 130
2578380 ATTTCTAGCC
* * *
2578390 TGTTACCCTACTACTTAGGGGGTTAAGGCTCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGT
1 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGT
* *
2578455 GATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTAAGGGGTTTAAAGTCTGTAAATTCGGCT
66 GATAAGATCTGTAAATTCAACCTGTTACCCTACTGCTAAGGGGGTTAAAGTCTGTAAATTCGGCT
*
2578520 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGT
1 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGT
* * * * *
2578585 GTTAAGATTTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAA
66 GATAAGATCTGTAAATTCAACCTGTTACCCTACTGCTAAGGGGGTTAA
2578633 GGCCCTTCGT
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 102 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (130 bp):
TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGT
GATAAGATCTGTAAATTCAACCTGTTACCCTACTGCTAAGGGGGTTAAAGTCTGTAAATTCGGCT
Found at i:2578726 original size:19 final size:19
Alignment explanation
Indices: 2578702--2578739 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2578692 CCTGTTACCC
2578702 TACTGCTTAGGAGTTTAAG
1 TACTGCTTAGGAGTTTAAG
*
2578721 TACTGCTTAGGGGTTTAAG
1 TACTGCTTAGGAGTTTAAG
2578740 GCCATCGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.37
Consensus pattern (19 bp):
TACTGCTTAGGAGTTTAAG
Found at i:2578801 original size:105 final size:106
Alignment explanation
Indices: 2578615--2578825 Score: 316
Period size: 105 Copynumber: 2.0 Consensus size: 106
2578605 CCTGTTACCC
* * * *
2578615 TACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTATTTCCTTACTGCTTAGGGTGATAAGAT
1 TACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGTGATAAGAT
*
2578680 CTGTGAATTCAACCTGTTACCCTACTGCTTAGGAGTTTAAG
66 CTGTAAATTCAACCTGTTACCCTACTGCTTAGGAGTTTAAG
* * *
2578721 TACTGCTTAGGGGTTTAAGG-CCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGAT
1 TACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGTGATAAGAT
* * *
2578785 CTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
66 CTGTAAATTCAACCTGTTACCCTACTGCTTAGGAGTTTAAG
2578826 GCCATCGCCT
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 75 0.80
106 19 0.20
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (106 bp):
TACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGTGATAAGAT
CTGTAAATTCAACCTGTTACCCTACTGCTTAGGAGTTTAAG
Found at i:2578866 original size:86 final size:86
Alignment explanation
Indices: 2578721--2579216 Score: 974
Period size: 86 Copynumber: 5.8 Consensus size: 86
2578711 GGAGTTTAAG
2578721 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
1 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
2578786 TGTAAATTTAGCCTGTTACCC
66 TGTAAATTTAGCCTGTTACCC
2578807 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
1 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
2578872 TGTAAATTTAGCCTGTTACCC
66 TGTAAATTTAGCCTGTTACCC
2578893 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
1 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
2578958 TGTAAATTTAGCCTGTTACCC
66 TGTAAATTTAGCCTGTTACCC
2578979 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
1 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
2579044 TGTAAATTTAGCCTGTTACCC
66 TGTAAATTTAGCCTGTTACCC
2579065 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
1 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
2579130 TGTAAATTTAGCCTGTTACCC
66 TGTAAATTTAGCCTGTTACCC
* *
2579151 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAATATC
1 TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
2579216 T
66 T
2579217 TTCGTCTTTG
Statistics
Matches: 408, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 408 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.36
Consensus pattern (86 bp):
TACTGCTTAGGGGTTTAAGGCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATC
TGTAAATTTAGCCTGTTACCC
Found at i:2579319 original size:130 final size:130
Alignment explanation
Indices: 2579107--2579346 Score: 356
Period size: 130 Copynumber: 1.8 Consensus size: 130
2579097 ATCTGTTTCC
* * ** * *
2579107 CTACTGCTTAGGGTGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
1 CTACTGCTTAGGGGGATAAGATCTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAGCC
*
2579172 CATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAATATCTTTCGTCTTTGATTTGCCCCA
66 CATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTTCGTCTTTGATTTGCCCCA
* *
2579237 CTACTGCTTAGGGGGATAAGATCTGT-AATCCGGTCTGTTACCCTACTACTTAGGGGTTTAAGAC
1 CTACTGCTTAGGGGGATAAGATCTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAG-C
* * *
2579301 CCTTCGTCTTCGATCTGTTTCCCTACTGTTTAGGGGGTTAAGATCT
65 CCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT
2579347 GGAAATTCAG
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
129 31 0.32
130 66 0.68
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (130 bp):
CTACTGCTTAGGGGGATAAGATCTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAGCC
CATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTTCGTCTTTGATTTGCCCCA
Done.